From: Grigory S. <sha...@gm...> - 2021-09-29 16:18:54
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Hi, The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear Grigory, > > Thank you so much, fixing this space solved the problem with > cryolo_1.7.6_installing (shame on me for this). > However, I tried to run the cryolo training and I obtained the same > previous error: > > eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json > -w 5 -g 0 1 -nc 4 -e 10 --fine_tune > 00022: Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json > -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. > 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 > 02:14:42.822982 > > Bellow, it is my current scipion.conf file > [PYWORKFLOW] > SCIPION_DOMAIN = pwem > SCIPION_FONT_NAME = Helvetica > SCIPION_GUI_REFRESH_IN_THREAD = False > SCIPION_LOG = ~/ScipionUserData/logs/scipion.log > SCIPION_LOGO = scipion_logo.gif > SCIPION_LOGS = ~/ScipionUserData/logs > SCIPION_NOTES_FILE = notes.txt > SCIPION_NOTIFY = True > SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ > SCIPION_SOFTWARE = ${SCIPION_HOME}/software > SCIPION_SUPPORT_EMAIL = sc...@cn... > SCIPION_TESTS = ${SCIPION_HOME}/data/tests > SCIPION_TESTS_CMD = scipion3 tests > SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests > SCIPION_TMP = ~/ScipionUserData/tmp > SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion > SCIPION_URL_SOFTWARE = > http://scipion.cnb.csic.es/downloads/scipion/software > SCIPION_URL_TESTDATA = > http://scipion.cnb.csic.es/downloads/scipion/data/tests > SCIPION_USER_DATA = ~/ScipionUserData > WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] > CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)" > > [PLUGINS] > CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 > CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 > CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta > CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 > CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 > CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 > CRYOLO_GENERIC_DENOISED_MODEL = > %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 > CRYOLO_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 > CRYOLO_NS_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 > CRYOSPARC_HOME = /home/impmc/ > CRYO_PROJECTS_DIR = scipion_projects > CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 > EMAN2SCRATCHDIR = /tmp > EMAN2_HOME = %(EM_ROOT)s/eman-2.91 > EM_ROOT = software/em > JANNI_GENERIC_MODEL = > %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 > MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 > MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 > MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 > MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 > PHENIX_HOME = %(EM_ROOT)s/phenix- > RELION_CUDA_LIB = /usr/local/cuda/lib64 > RELION_HOME = %(EM_ROOT)s/relion-3.1.2 > XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src > XMIPP_HOME = %(EM_ROOT)s/xmipp > > > Thanks again. > > ------------------------------ > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Wednesday, September 29, 2021 5:51:06 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > Hello Carlos, > > to start, you are missing a space between eval and the rest in: > CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)" > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > >> Dear Grigory, >> >> Thanks for the message. The all output is bellow: >> >> Scipion v3.0.9 - Eugenius >> Building scipion-em-sphire ... >> /home/impmc/scipion/.scipion3/bin/python -m pip install >> scipion-em-sphire==3.0.7 >> Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com >> Requirement already satisfied: scipion-em-sphire==3.0.7 in >> ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) >> Requirement already satisfied: scipion-em in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-em-sphire==3.0.7) (3.0.13) >> Requirement already satisfied: biopython==1.76 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-em->scipion-em-sphire==3.0.7) (1.76) >> Requirement already satisfied: tifffile in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) >> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-em->scipion-em-sphire==3.0.7) (3.0.17) >> Requirement already satisfied: numpy in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) >> Requirement already satisfied: mpi4py<=3.0.3 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) >> Requirement already satisfied: configparser<=5.0.2 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) >> Requirement already satisfied: psutil<=5.8.0 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) >> Requirement already satisfied: pillow<=8.2.0 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) >> Requirement already satisfied: bibtexparser<=1.2.0 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) >> Requirement already satisfied: requests<=2.25.1 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) >> Requirement already satisfied: matplotlib==3.2.2 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) >> Requirement already satisfied: tkcolorpicker<=2.1.3 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) >> Requirement already satisfied: cycler>=0.10 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (0.10.0) >> Requirement already satisfied: python-dateutil>=2.1 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (2.8.1) >> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 >> in ./scipion/.scipion3/lib/python3.8/site-packages (from >> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (2.4.7) >> Requirement already satisfied: kiwisolver>=1.0.1 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (1.3.1) >> Requirement already satisfied: future>=0.16.0 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (0.18.2) >> Requirement already satisfied: six in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (1.16.0) >> Requirement already satisfied: certifi>=2017.4.17 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (2020.12.5) >> Requirement already satisfied: urllib3<1.27,>=1.21.1 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (1.26.4) >> Requirement already satisfied: chardet<5,>=3.0.2 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (4.0.0) >> Requirement already satisfied: idna<3,>=2.5 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (2.10) >> Done (0.84 seconds) >> Building cryolo-1.7.6 ... >> Skipping command: wget -nv -c -O >> /home/impmc/scipion/software/em/void.tgz.part >> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz >> mv -v /home/impmc/scipion/software/em/void.tgz.part >> /home/impmc/scipion/software/em/void.tgz >> All targets exist. >> Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 >> All targets exist. >> Skipping command: tar -xf void.tgz -C cryolo-1.7.6 >> All targets exist. >> cd /home/impmc/scipion/software/em/cryolo-1.7.6 >> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda >> python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 >> intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install >> cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed >> /bin/sh: 1: evalexport >> CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' >> export _CE_M='' >> export _CE_CONDA='' >> export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' >> >> # Copyright (C) 2012 Anaconda, Inc >> # SPDX-License-Identifier: BSD-3-Clause >> >> __add_sys_prefix_to_path() { >> # In dev-mode CONDA_EXE is python.exe and on Windows >> # it is in a different relative location to condabin. >> if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then >> SYSP=$(\dirname "${CONDA_EXE}") >> else >> SYSP=$(\dirname "${CONDA_EXE}") >> SYSP=$(\dirname "${SYSP}") >> fi >> >> if [ -n "${WINDIR+x}" ]; then >> PATH="${SYSP}/bin:${PATH}" >> PATH="${SYSP}/Scripts:${PATH}" >> PATH="${SYSP}/Library/bin:${PATH}" >> PATH="${SYSP}/Library/usr/bin:${PATH}" >> PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" >> PATH="${SYSP}:${PATH}" >> else >> PATH="${SYSP}/bin:${PATH}" >> fi >> \export PATH >> } >> >> __conda_exe() ( >> __add_sys_prefix_to_path >> "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" >> ) >> >> __conda_hashr() { >> if [ -n "${ZSH_VERSION:+x}" ]; then >> \rehash >> elif [ -n "${POSH_VERSION:+x}" ]; then >> : # pass >> else >> \hash -r >> fi >> } >> >> __conda_activate() { >> if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then >> # Handle transition from shell activated with conda <= 4.3 to a >> subsequent activation >> # after conda updated to >= 4.4. See issue #6173. >> PS1="$CONDA_PS1_BACKUP" >> \unset CONDA_PS1_BACKUP >> fi >> \local ask_conda >> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return >> \eval "$ask_conda" >> __conda_hashr >> } >> >> __conda_reactivate() { >> \local ask_conda >> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || >> \return >> \eval "$ask_conda" >> __conda_hashr >> } >> >> conda() { >> \local cmd="${1-__missing__}" >> case "$cmd" in >> activate|deactivate) >> __conda_activate "$@" >> ;; >> install|update|upgrade|remove|uninstall) >> __conda_exe "$@" || \return >> __conda_reactivate >> ;; >> *) >> __conda_exe "$@" >> ;; >> esac >> } >> >> if [ -z "${CONDA_SHLVL+x}" ]; then >> \export CONDA_SHLVL=0 >> # In dev-mode CONDA_EXE is python.exe and on Windows >> # it is in a different relative location to condabin. >> if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then >> PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" >> else >> PATH="$(\dirname "$(\dirname >> "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" >> fi >> \export PATH >> >> # We're not allowing PS1 to be unbound. It must at least be set. >> # However, we're not exporting it, which can cause problems when >> starting a second shell >> # via a first shell (i.e. starting zsh from bash). >> if [ -z "${PS1+x}" ]; then >> PS1= >> fi >> fi >> >> conda activate base: not found >> Traceback (most recent call last): >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >> line 470, in <module> >> main() >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >> line 293, in main >> installPluginMethods() >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", >> line 232, in installPluginMethods >> plugin.installBin({'args': ['-j', numberProcessor]}) >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >> line 166, in installBin >> environment.execute() >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 748, in execute >> self._executeTargets(targetList) >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 690, in _executeTargets >> tgt.execute() >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 221, in execute >> command.execute() >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 161, in execute >> assert glob(t), ("target '%s' not built (after " >> AssertionError: target >> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >> Error at main: target >> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >> >> ------------------------------ >> *From: *"Grigory Sharov" <sha...@gm...> >> *To: *"scipion-users" <sci...@li...> >> *Sent: *Wednesday, September 29, 2021 5:33:09 PM >> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >> Cryolo >> >> Dear Carlos, >> given the fact that the installation has failed, could you attach all >> output after "scipion3 installp -p scipion-em-sphire" command? >> >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < >> car...@so...> wrote: >> >>> Dear all, >>> >>> I'm facing some problems using cryolo training at Scipion. >>> I found the following error: >>> >>> *Protocol failed: Command ' source >>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate >>> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 >>> --fine_tune' returned non-zero exit status 127.* >>> >>> I saw some discussion about that at Scipion lists, but I'm still little >>> lost in how to fix it. >>> In my scipion.conf file, I inserted >>> *CONDA_ACTIVATION_CMD = source >>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * >>> or even >>> CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>> shell.bash hook)" >>> (I saw these pathways in my bash.rc) >>> >>> Moreover, when I try to install cryolo using command line (scipion3 >>> installp -p scipion-em-sphire), the following error apears: >>> *AssertionError: target >>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>> built (after running 'source >>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n >>> cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 >>> numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate >>> cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch >>> cryolo_1.7.6_installed')* >>> >>> I am not sure if these errors are related and hinder performing cryolo >>> in Scipion. >>> I have conda installed in the computer and I'm able to use cryolo 1.8 >>> outside from Scipion in the same computer (using *source activate >>> cryolo *command). >>> >>> Anyone know what I'm doing wrong? >>> Thanks in advance, >>> Carlos. >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |